I have to simulate carbohydrate-protein complex on GROMACS. I have used GLYCAM webserver to generate a trisaccharide. Then I used acpype of Ambertools21 to prepare carbohydrate ligand using GLYCAM_06j force field. It is giving me outputs as .gro and .top file. I need .itp file to run it on GROMACS. If I use .top then it gives me the following error (attach file). I am new to MD simulations. Is there a way to convert .pdb or .top file to itp? Pdb2gmx is useless in this matter.
Saleha Hafeez
Assalam o alaikum wa rahmatullahi wa barkatahu
First of all prepare your ligand topology properly and very carefully prepare protein-ligand file
@waseem ahmed ansari
Is there a way to get itp file of ligand using ambertools?
Saleha Hafeez
You can go through SWISSPARAM
https://www.swissparam.ch/
Dear Saleha Hafeez
If you open the .top file you posted you will find the parameters for your molecule, starting with
[ moleculetype ]
and closing with the values under
[ dihedrals ] ; impropers
that is, excluding what comes from [ system ] and later on. Try to open a .itp file of GROMACS, you'll see that the structure is the same. I think you can just copy paste these sections into an .itp file, then build the .top file of your system by properly including (#include statement) the forcefield parameters and the .itp file for your ligand.
@nicola piasentin thank you.
I have deleted lines before atomtypes and after dihedral (system). It is working now.
@Saleha Hafeez use acpype too to generate .itp parameters file for AMBER forcefiled https://alanwilter.github.io/acpype
The tool also provides .itp files for OPLS amd CHARMM forcefields too. However, i havent tested them.
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